Either the corn or the recipe you're using could be the problem. Are you using fresh corn and grating the kernels off the cob yourself? Many varieties of supersweet corn have a very clear, watery juice in them. More traditional varieties have a milkier, starchier juice, which thickens like a sauce when heated above 150°F (65°C). If you can find corn with the milkier juice, that may solve your problem.

The lovely women who dedicated their careers to producing Joy of Cooking, Irma S. Rombauer and Marion Rombauer Becker, address this issue in one of their showcase recipes - Corn Pudding Cockaigne. They found corn to differ significantly with the season, so it was hard to be specific in the recipe. Early in the season, they said, the corn might be so watery it was necessary to add a beaten egg to the dish. Towards autumn, when the corn was dryer, they might have to increase the amount of liquid in the recipe to compensate.

It is possible, though, that the recipe you're using just includes too much liquid. The solutions in that case are to add less liquid, to cook away more of the liquid, add some means of thickening the mixture - or simply find another recipe. Hey! How about Corn Pudding Cockaigne?